4HP8 | pdb_00004hp8

Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP

• PDB DOI: https://doi.org/10.2210/pdb4HP8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-23 Released: 2012-11-07 
• Deposition Author(s): Vetting, M.W., Bouvier, J.T., Groninger-Poe, F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium Tumefaciens (target EFI-506435) with bound NADP

Vetting, M.W., Bouvier, J.T., Groninger-Poe, F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 53.09 kDa 
• Atom Count: 4,371 
• Modeled Residue Count: 491 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-deoxy-D-gluconate 3-dehydrogenase	A, B	247	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: kduD, Atu3141
UniProt
Find proteins for A9CEQ9 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CEQ9  Go to UniProtKB:  A9CEQ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.022	α = 90
b = 93.022	β = 90
c = 109.285	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Vetting, M.W., Bouvier, J.T., Groninger-Poe, F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description